Unclear. One theory is that this is a native Japanese term, with the su reading somehow related to the way that very sour things cause one to pucker.

Given that vinegar was historically introduced to Japan in the 300-400s from China, another possibility is that the su reading is from Middle Chinese酢 or 醋 instead, and that this naturalized and came to be regarded as a native kun'yomi rather than a Chinese-derived on'yomi. Compare modern Mandarin reading cù or Cantonesecou3.

酢 (す)でも酒塩 (さかしお)でも ‎(su de mo sakashio de mo), 酢 (す)でも蒟蒻 (こんにゃく)でも ‎(su de mo konnyaku de mo): (used with a negative verb): Something that cannot be done in the usual fashion, or cannot be done easily.